# Simulating a protein with two chains and two identical ligands

**URL:** <https://gromacs.bioexcel.eu/t/simulating-a-protein-with-two-chains-and-two-identical-ligands/4121>\
**Category:** User discussions\
**Created:** [May 6, 2022, 1:49pm UTC](https://gromacs.bioexcel.eu/t/simulating-a-protein-with-two-chains-and-two-identical-ligands/4121 "2022-05-06T13:49:58Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![Kash9](https://avatars.discourse-cdn.com/v4/letter/k/df788c/32.png) [@Kash9](https://gromacs.bioexcel.eu/u/Kash9)\
**Post date:** [May 6, 2022, 1:49pm UTC](https://gromacs.bioexcel.eu/t/simulating-a-protein-with-two-chains-and-two-identical-ligands/4121/1 "2022-05-06T13:49:58Z")

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GROMACS version:  
GROMACS modification: Yes/No  
Here post your question

Hi all,

I’m simulating a protein with two chains (A + B). Each chain has a ligand bound to it. Both ligands are identical. I was following the protein-ligand tutorial on gromacs. When I visualise my processed complex file (complex.gro), I can see both ligand are overlapping rather than bound to their respective chains. Is there a way I can correct this? Any help would be appreciated.

Many thanks,

Akash

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**Author:** ![jalemkul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/jalemkul/32/18_2.png) [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)\
**Post date:** [May 9, 2022, 5:23pm UTC](https://gromacs.bioexcel.eu/t/simulating-a-protein-with-two-chains-and-two-identical-ligands/4121/2 "2022-05-09T17:23:08Z")

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You probably copied the same ligand twice.